Contacts of the helix formed by residues 82 - 88 (chain H) in PDB entry 3EXG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 82 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H TYR* 3.6 20.0 - - - +
80H PHE* 3.8 8.7 - - - +
81H MET* 1.3 84.3 - - + +
83H PHE* 1.3 63.6 + - - +
84H ASN* 2.9 31.8 + - - +
85H PHE* 2.9 36.8 + - + +
86H SER 3.7 1.6 + - - -
117H PRO* 3.4 18.2 - - + -
128H HIS* 5.1 6.5 - - + +
173H GLU* 5.8 0.9 - - - +
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Residues in contact with PHE 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H PHE* 3.9 17.0 - + + -
82H THR* 1.3 69.1 - - - +
84H ASN* 1.3 66.6 + - - +
86H SER* 2.8 40.8 + - - -
87H MET 3.8 0.7 + - - -
93H VAL* 6.4 0.2 - - + -
114H PHE* 3.7 31.4 - - + -
115H ARG* 3.7 3.4 - - - -
116H GLY* 3.3 36.1 - - - -
117H PRO 3.1 13.0 + - - -
118H ASN* 3.8 9.6 - - + +
132H PHE* 3.5 27.7 - - + -
136H TYR* 3.7 18.2 - + - -
168H VAL* 3.7 24.0 - - + -
169H VAL 3.5 10.8 - - - -
170H LEU* 3.7 13.0 - - + -
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Residues in contact with ASN 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E ILE* 5.1 2.3 - - + +
95F ASN* 4.5 3.2 + - - +
99F LYS* 5.0 0.7 + - - -
82H THR* 2.9 25.5 + - - +
83H PHE* 1.3 77.6 - - - +
85H PHE* 1.3 69.0 + - + +
86H SER 3.0 1.7 + - - -
87H MET* 3.2 27.6 + - + +
88H GLN* 5.5 0.3 - - - +
118H ASN* 6.1 1.2 - - - +
119H GLY 5.1 3.2 + - - +
127H GLN 3.5 24.6 - - - +
128H HIS* 3.2 24.5 + - - +
129H SER 3.3 3.3 + - - +
130H GLN* 3.1 38.5 + - - +
132H PHE* 3.6 10.6 - - - -
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Residues in contact with PHE 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E PHE* 6.1 0.2 - + - -
136E GLY 4.3 4.5 - - - -
137E ILE* 3.7 36.1 - - + -
138E VAL* 5.5 4.9 - - + -
28H GLU* 5.4 1.3 - - - -
59H GLU* 3.5 41.2 - - + +
80H PHE* 4.7 0.9 - - + -
81H MET* 3.3 44.0 - - + +
82H THR* 2.9 28.2 + - + +
84H ASN* 1.3 77.2 - - + +
86H SER* 1.3 60.1 + - - +
87H MET 3.2 1.0 + - - -
88H GLN* 3.6 17.0 + - - +
128H HIS* 3.5 31.4 - + - -
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Residues in contact with SER 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H PHE* 3.5 44.4 - - - -
82H THR 3.7 1.4 + - - -
83H PHE* 2.8 27.5 + - - -
85H PHE* 1.3 74.6 - - - +
87H MET* 1.3 58.1 + - - +
88H GLN 3.0 3.1 - - - -
89H ALA* 2.9 20.3 + - - +
90H ILE* 3.0 11.4 + - - +
132H PHE* 5.4 1.0 - - - -
136H TYR* 2.5 27.2 + - - -
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Residues in contact with MET 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F MET 4.0 4.9 - - - +
88F GLN 5.2 0.3 - - - +
90F ILE* 3.8 20.8 + - + +
91F ASP* 3.9 24.3 + - + +
94F ILE* 4.0 25.4 - - - -
95F ASN* 3.0 35.9 - - - +
99F LYS* 4.9 0.2 - - - +
84H ASN* 3.2 16.6 + - + +
86H SER* 1.3 78.9 + - - +
88H GLN* 1.3 62.0 + - - +
89H ALA 3.2 0.5 + - - -
90H ILE* 3.3 14.9 + - + +
130H GLN* 3.4 23.3 - - - +
132H PHE* 3.6 31.6 - - + -
135H TRP* 4.1 15.3 - - + -
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Residues in contact with GLN 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ILE* 3.5 26.4 - - + +
138E VAL 3.9 0.3 - - - +
172E GLN* 3.3 32.2 + - - +
174E GLN* 3.7 12.6 + - - -
60F MET* 3.8 28.6 - - + +
88F GLN* 4.6 4.5 - - - +
91F ASP* 4.1 9.7 - - + +
177G GLU* 5.2 2.2 + - - -
59H GLU* 3.9 18.3 + - + +
60H MET* 3.3 39.2 - - + +
84H ASN 5.5 0.4 - - - +
85H PHE* 3.7 16.8 - - - +
86H SER 3.0 0.2 - - - -
87H MET* 1.3 80.4 - - + +
89H ALA* 1.3 56.4 + - - +
90H ILE 3.5 0.2 - - - -
91H ASP 5.0 0.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il